animals Article Insight into the Current Genetic Diversity and Population Structure of Domestic Reindeer (Rangifer tarandus) in Russia Veronika Kharzinova 1,* , Arsen Dotsev 1, Anastasiya Solovieva 1, Olga Sergeeva 2, Georgiy Bryzgalov 3, Henry Reyer 4 , Klaus Wimmers 4 , Gottfried Brem 1,5 and Natalia Zinovieva 1,* 1 L.K. Ernst Federal Science Center for Animal Husbandry, 60, Settl. Dubrovitsy, Podolsk Municipal District, 142132 Moscow Region, Russia; [email protected] (A.D.); [email protected] (A.S.); [email protected] (G.B.) 2 Research Institute of Agriculture and Ecology of the Arctic—Branch of the FRC KSC SB RAS, 663302 Norilsk, Russia; [email protected] 3 Magadan Research Institute of Agricultural, 685000 Magadan, Russia; [email protected] 4 Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Mecklenburg-Vorpommern, 18196 Dummerstorf, Germany; [email protected] (H.R.); [email protected] (K.W.) 5 Institut für Tierzucht und Genetik, University of Veterinary Medicine (VMU), Veterinärplatz, A-1210 Vienna, Austria * Correspondence: [email protected] (V.K.); [email protected] (N.Z.); Tel.: +7-4967651104 (V.K.); +7-4967651404 (N.Z.) Received: 6 July 2020; Accepted: 28 July 2020; Published: 30 July 2020 Simple Summary: Reindeer herding is the most important agricultural sector of the Russian Far North, representing the local genetic resources that compose original genetic wealth for the indigenous Arctic ethnic groups, which has maintained their life in harsh conditions of the area for many years. Conservation about and further rational use of such resources are very difficult without taking into account genetic diversity. Here, for the first time, the current genetic composition of the four officially recognized reindeer breeds and their ecotypes inhabiting the area from the Kola Peninsula in the west to the Chukotka region in the east are described using a single-nucleotide polymorphism (SNP) array. Our findings reveal the genetic uniqueness of each breed, formed by the consequences of ecological processes, internal gene flow, breeding practices, and geographical features. The obtained results will assist the ongoing breeding policy to develop accurate programs to preserve genetic resources of this essential element of Russia’s Far North ecosystem. Abstract: To examine the genetic diversity and population structure of domestic reindeer, using the BovineHD BeadChip, we genotyped reindeer individuals belonging to the Nenets breed of the five main breeding regions, the Even breed of the Republic of Sakha, the Evenk breed of the Krasnoyarsk and Yakutia regions, and the Chukotka breed of the Chukotka region and its within-breed ecotype, namely, the Chukotka–Khargin, which is bred in Yakutia. The Chukotka reindeer was shown to have the lowest genetic diversity in terms of the allelic richness and heterozygosity indicators. The principal component analysis (PCA) results are consistent with the neighbor-net tree topology, dividing the reindeer into groups according to their habitat location and origin of the breed. Admixture analysis indicated a genetic structuring of two groups of Chukotka origin, the Even breed and most of the geographical groups of the Nenets breed, with the exception of the Murmansk reindeer, the gene pool of which was comprised of the Nenets and apparently the native Sami reindeer. The presence of a genetic component of the Nenets breed in some reindeer inhabiting the Krasnoyarsk region was detected. Our results provide a deeper insight into the current intra-breeding reindeer genetic diversity, which is an important requirement for future reindeer herding strategies and for animal adaptation to environmental changes. Animals 2020, 10, 1309; doi:10.3390/ani10081309 www.mdpi.com/journal/animals Animals 2020, 10, 1309 2 of 18 Keywords: reindeer; breeds; genetic diversity; population structure; SNP 1. Introduction Reindeer (Rangifer tarandus L. 1758) is an ungulate that inhabits the whole circumpolar area of the northern hemisphere, and it is the last animal to be domesticated by humans [1,2]. There are currently about 2.5 million domesticated reindeer located across nine countries, among which the Russian Federation is the largest reindeer breeder. Reindeer herding is the only agricultural sector in the Arctic region, which is concentrated in 18 Russian Federation subjects of four federal districts [3]. The century-long process of purposeful implementation of the particular sets of practices in these districts, as well as scientifically based selection and the pure-line breeding within the Soviet Union era, are reflected in the creation of unique populations that differ from each other not only in exterior and constitution, but also in the nature of their phenotypic traits. Subsequently, in 1985, these differences were entrenched in order No. 212 of the Russian Ministry of Agriculture (formerly the USSR Ministry of Agriculture) by the official recognition of four reindeer breeds: Nenets, Even, Evenk, and Chukotka [4]. The Nenets breed (Figure S1) is the largest in Russia by number (1,300,800 heads) and pasture territory (110 million ha) [5]. These reindeer are of an average size with rather well-defined working capacities and high reproductive performance [6]. The Evenk breed (Figure S2) is considered to be the oldest, with the total stock amounting to no more than 20,000 animals [7,8]. These animals are known for their high load-carrying capacity and endurance, and are still extensively used for transport [9]. The reindeer of the Even breed (Figure S3) are well adapted to mountainous areas, occupying alpine pastures in summer and river valleys and depressions in winter [9]. The total stock of this breed amounts to approximately 154,000 individuals. A high meat production, as well as a high adaptation to the environmental conditions of the arctic and subarctic tundra and their well-developed herd instinct are inherent to the Chukotka reindeer breed (Figure S4), with the total stock of this breed amounting to 202,100 individuals [9,10]. Furthermore, due to differences in natural and economic conditions, specific feeding, and breeding systems, several within-breed ecotypes have been developed in different areas [11]. Yuzhakov et al. [12] highlighted several ecotypes within the Nenets breed, division into which is based on phenotypic traits (i.e., fawning term, constitutional peculiarities, body weight, and color). Four ecotypes of animals are distinguished in the Chukotka breed, as referred to by Baskin [13], three of which are bred in areas of the Kamchatka Peninsula and the Chukotka region, while the fourth one inhabits two encampments of the tundra zone of Yakutia and is called Khargin. However, these reindeer had already been differentiated by their conformation, feeding habits, and behavior from their Chukotka conspecifics. Moreover, considering the country’s economy, regional reindeer herding is concentrated in the seven regional clusters, which cover approximately 90% of all of the Russian reindeer, including the Murmansk region (i.e., European Russia, tundra reindeer herding on the Kola Peninsula by Saami and Komi with mixed Saami–Nenets reindeer), the Nenets Autonomous district and the Arkhangelsk region (European Russia, mainly tundra reindeer herding by European Nenets with the Nenets reindeer), the Komi Republic (European Russia, reindeer herding at the forest–tundra margin and mountains by Komi and Nenets with the Nenets reindeer), Yamalo-Nenets Autonomous district (West Siberia, mainly tundra reindeer herding, but also taiga, forest–tundra margin, and mountain types by the Nenets, Khanty, and Komi with the Nenets reindeer), the Sakha Republic (Yakutia; East Siberia, tundra, taiga, and forest types, by the Evenk (taiga) the Even (taiga, mountain, and tundra), the Sakha and Dolgans (mainly tundra) with the Evenk, Even, and Khargin reindeer), the Chukotka region (Far East, tundra type, mainly by Chukchi with Chukotka reindeer), and the Koryak Autonomous district (Far East, forest–tundra margin by Koryaks with Chukotka and Even reindeer) [14]. Despite the widespread occurrence of the domestic reindeer in the regions of the Russian Far North, the population census size over the last few decades has decreased. The first accurate registration Animals 2020, 10, 1309 3 of 18 of the reindeer population was carried out in 1926–1927, with the number of heads being 2,202,700, which then declined with collectivization to 1.4 million, stabilized after World War II, and later climbed back to very high levels of more than 2.1 million during the three sovkhoz decades (1961–1993) [14,15]. The recent drastic decline, which led authors such as Baskin [16] to consider domestic reindeer herding as being on the edge of extinction, happened after the Soviet Union collapse, reaching numbers lower than those of the early 20th century. As of 1 January 2019, the domestic reindeer population size was confirmed to be 1,702,000 livestock units [3]. The negative effects of the domestic reindeer decline might have reflected on processes such as genetic drift, gene flow, and natural selection, which, in turn, affect the distribution of the genetic diversity and structuring across a species range [17]. According to Lewis et al. [18], the study of the genetic diversity found within domestic animals can result in the most complete representation of species domestication, as well as mammalian biology and evolution. Additionally, the insight into the genetic variability pattern of breeds, especially